mrtrix3.rb

class Qt5Requirement < Requirement
  fatal true
  satisfy :build_env => false do
    if File.file?("#{HOMEBREW_PREFIX}/opt/qt5/bin/qmake")
      @qmake = which("#{HOMEBREW_PREFIX}/opt/qt5/bin/qmake")
    else
      @qmake = which('qmake')
    end
    @qmake
  end

  env do
    ENV.append_path 'PATH', File.dirname(@qmake)
  end

  def message
    message = <<-EOS
      Homebrew was unable to find an installation of Qt 5. You can install it for instance via homebrew:


      brew update
      brew install qt5


    EOS
  end
end



class Mrtrix3 < Formula
  desc "MRtrix3: tools to perform various types of diffusion MRI analyses."

  homepage "http://mrtrix.org"

  url "https://github.com/MRtrix3/mrtrix3.git"

  version  '3.0.2-48-g63d94827'
  revision 0
  # devel do
  #   url 'https://github.com/MRtrix3/mrtrix3.git', :branch => 'master', :revision => 'bogus474279845b7e79fc2b5ffad'
  #   version '0.3_dev'
  # end

  option "with-stable", "Install latest tagged stable version. Default is last commit on master branch."
  option "test", "Run tests after installation."
  option "with-assert", "Build with assert statements (executables are slower)."
  option "with-debug", "Build with debug statements (executables are slower)."
  option "with-mrconvert", "Build mrconvert, no other binaries unless stated"
  option "with-mrinfo", "Build mrinfo, no other binaries unless stated"
  option "with-mrview", "Build mrview, no other binaries unless stated"
  option "without-multithreaded_build", "This is useful if your computer has many cores but not enough RAM to build MRtrix using multiple threads. Alternatively, set the environment variable HOMEBREW_NUMBER_OF_PROCESSORS=1"
  option "without-matlab", "Do not add MRtrix scripts to matlab path."
  option "with-copy_src_from_home", "Use MRtrix3 source code from ~/mrtrix3. This settting is for developers and testing purposes!"

  depends_on "python" => :recommended
  depends_on "eigen" => :build
  depends_on "fftw" => :recommended
  depends_on "libtiff" => :recommended
  depends_on "pkg-config"
  # depends_on "qt5" # not used as users might want to use an existing qt or install mrtrix without a GUI
  depends_on Qt5Requirement => :recommended

  conflicts_with "mrtrix3_0rc3", :because => "tagged version (mrtrix3@0rc3) conflicts with non-tagged version of mrtrix3 (this)."

  def execute (cmd)
    # verbose alternative to: system cmd
    require 'pty'
    raw = ''
    PTY.spawn(cmd) do |stdout_err, stdin, pid|
      begin
        while (char = stdout_err.getc)
          raw << char
          print char
        end
      rescue Errno::EIO # always raised when PTY runs out of input
      ensure
        Process.waitpid pid # Wait for PTY to complete before continuing
      end
    end
    return raw
  end

  def set_matlab_path ()
    matlab_add = <<-EOS
import os, glob, sys, subprocess

# Trick out homebrew's overwrite of USER
p = subprocess.Popen('whoami', shell = True, stdout=subprocess.PIPE)
me = p.stdout.readline().rstrip()
p.wait()

comment='% MRtrix3 PATH automatically generated by homebrew installation formula - do NOT modify:'
set_path = "addpath('#{prefix}/matlab')" + os.linesep

def path_has_been_set(startup):
    if not os.path.isfile(startup):
        return False
    with open (startup, "r") as inp:
        for iline, line in enumerate(inp):
            if comment in line:
                nl = next(inp)
                if not 'mrtrix' in nl.lower():
                    raise Exception ('matlab startup file ' + startup + ' has been modified. aborting. ' + nl)
                return iline + 1
    return 0

matlab_bins = glob.glob("/Applications/MATLAB_R20*/bin/matlab")
if not len(matlab_bins):
    print ("WARNING: no Matlab binary found. Not adding MRtrix to Matlab startup path")
    sys.exit(0)

startup_locations = []
for bin in matlab_bins:
    matlab_root = os.path.split(os.path.split(bin)[0])[0]
    startup_locations.append(os.path.join(matlab_root, "toolbox", "local", "startup.m"))

userdir = os.path.join('/Users',me,'Documents','MATLAB')
if os.path.isdir(userdir):
    startup_locations.append(os.path.join(userdir,"startup.m"))
else:
  print userdir + " not found"

is_set = 0
for startup in startup_locations:
    try:
        pline = path_has_been_set(startup)
        if pline:
            with open (startup, "r") as inp:
                sf = inp.readlines()
                sf[pline] = set_path + os.linesep
            with open (startup, "w") as inp:
                inp.write(''.join(sf))
            print ("updated mrtrix path in " + startup)
        else:
            with open (startup, "a") as inp:
                inp.write(comment + os.linesep + set_path + os.linesep)
            print ("added mrtrix path to " + startup)
        is_set += 1
    except:
        print "WARNING: could not set mrtrix path in Matlab startup file: " + startup
if not (is_set):
    raise Exception('could not set mrtrix path in any Matlab startup file')
EOS
      open('matlab_add.py', 'w') do |f|
        f.puts matlab_add
      end
      system "python", "matlab_add.py"
      rm 'matlab_add.py'
  end

  def install
    puts "PATH:"
    puts ENV["PATH"]
    if ENV["PATH"].downcase.include? "anaconda"
      puts "warning: anaconda found in PATH. You might want to exclude those directories from you PATH."
    end
    xcodeerror=`xcodebuild 2>&1`
    # puts xcodeerror
    if xcodeerror.include? "tool 'xcodebuild' requires Xcode"
      puts "\nxcodebuild failed with the error message:"
      puts xcodeerror
      puts "If the command line tools were installed before Xcode, you can fix this with:"
      puts "sudo xcode-select -s /Applications/Xcode.app/Contents/Developer"
      raise 'command line tools failure'
    end

    if build.with? "stable"
      system "git", "reset", "--hard", "origin/master"
      system "git", "fetch", "-t"
      latesttag = `git describe --tags --abbrev=0`.strip
      system "git", "checkout", "#{latesttag}"
    end

    if build.without? "matlab"
      print "ignoring Matlab"
    else
      begin
        set_matlab_path()
      rescue BuildError => bang
        print "Unable to set Matlab path: " + bang.to_s + "\n"
      end
    end

    if !ENV['HOMEBREW_NUMBER_OF_PROCESSORS'].nil? # ENV option: HOMEBREW_NUMBER_OF_PROCESSORS
      ENV['NUMBER_OF_PROCESSORS'] = ENV['HOMEBREW_NUMBER_OF_PROCESSORS']
    end
    if build.without? "multithreaded_build"
      ENV["NUMBER_OF_PROCESSORS"] = "1"
    end

    conf = [ "./configure"]
    if build.without? "qt5"
      conf.push("-nogui")
    end
    if build.with? "assert"
      conf.push("-assert")
    end
    if build.with? "debug"
      conf.push("-debug")
    end

    if build.with? "copy_src_from_home"
      me = `whoami`.strip
      external_mrtrix_src_dir = "/Users/"+me+"/mrtrix3"
      if not File.directory?("#{external_mrtrix_src_dir}")
        raise "not found: "+external_mrtrix_src_dir+". --with-copy_src_from_home is intended for developers only"
      end
      execute("rm -r *")
      execute("cp -r "+external_mrtrix_src_dir+"/* ./")
    end

    execute (conf.join(" "))
    bin.mkpath()
    pkgshare.mkpath()
    cp "LICENCE.txt", "#{prefix}/"
    cp "LICENCE.txt", "#{pkgshare}/"

    system "git", "reset", "head"
    system "git", "log", "-1"
    system "git", "describe", "--always", "--dirty"

    env = %x[env]
    puts "shared path: #{pkgshare}"
    File.open("#{pkgshare}/env", 'w') { |file| file.write(env) }

    if File.directory?("release") # pre tag 0.3.16

      system "mkdir", "#{prefix}/lib"
      system "mkdir", "#{prefix}/release"
      system "ln", "-s", "#{prefix}/bin", "#{prefix}/release/bin"

      system "mkdir", "#{prefix}/matlab"
      cp_r 'matlab/.', "#{prefix}/matlab/"

      system "mkdir", "#{prefix}/icons"
      cp_r 'icons/.', "#{prefix}/icons/"

      # copy and link scripts
      system "mkdir", "#{prefix}/scripts"
      cp_r 'scripts/.', "#{prefix}/scripts/"
      # find scripts that have lib.app.initParser and add others manually
      scripts = `find "#{prefix}/scripts" -type f ! -name "*.*" -maxdepth 1`
      scripts = scripts.split(" ")
      scripts = scripts.uniq.sort
      for scrpt in scripts
        print "linking "+Pathname(scrpt).each_filename.to_a[-1]+"\n"
        # bin.install_symlink prefix/"scripts/"Pathname(scrpt).each_filename.to_a[-1]
        system "ln", "-s", scrpt, "#{prefix}/bin/"+Pathname(scrpt).each_filename.to_a[-1]
      end

      bld = [ "./build"]
      if build.with? "mrconvert"
        bld.push("release/bin/mrconvert")
      end
      if build.with? "mrinfo"
        bld.push("release/bin/mrinfo")
      end
      if build.with? "mrview"
        bld.push("release/bin/mrview")
      end
      execute (bld.join(" "))

      # This has to be before bin.install or else binaries are not in place.
      if build.with? "test"
        tst = [ "./run_tests"]
        if build.with? "mrconvert"
          tst.push("mrconvert")
        end
        execute (tst.join(" "))
        cp "testing.log", pkgshare
        print "Testing done. Testlog is in #{pkgshare}\n"
      end

      execute("git rev-parse HEAD > #{pkgshare}/git_hash")
      bin.install Dir["release/bin/*"]
      cp_r 'release/lib/.', "#{prefix}/lib/"
      cp "release/config", pkgshare

    else # >= tag_0.3.16
      cp "config", pkgshare
      cp "configure.log", pkgshare

      system "mkdir", "#{prefix}/matlab"
      cp_r 'matlab/.', "#{prefix}/matlab/"

      system "mkdir", "#{prefix}/icons"
      cp_r 'icons/.', "#{prefix}/icons/"

      bld = [ "./build"]
      if build.with? "mrconvert"
        bld.push("bin/mrconvert")
      end
      if build.with? "mrinfo"
        bld.push("bin/mrinfo")
      end
      if build.with? "mrview"
        bld.push("bin/mrview")
      end
      execute (bld.join(" "))


      # This has to be before bin.install or else binaries are not in place.
      if build.with? "test"
        tst = [ "./run_tests"]
        if build.with? "mrconvert"
          tst.push("mrconvert")
        end
        execute (tst.join(" "))
        cp "testing.log", pkgshare
        print "Testing done. Testlog is in #{pkgshare}\n"
      end


      execute("git rev-parse HEAD > #{pkgshare}/git_hash")
      bin.install Dir["bin/*"]
      system "mkdir", "#{prefix}/lib"
      cp_r 'lib/.', "#{prefix}/lib/"
      cp "config", pkgshare

    end

    # TODO: mrtrix_bash_completion

    print "Installation done. MRtrix3 lives in #{prefix}\n"
    print "For more information go to http://mrtrix.readthedocs.io\n"

  end

  # test do
  #   if build.with? "copy_src_from_home"
  #     me = `whoami`.strip
  #     external_mrtrix_src_dir = "/Users/"+me+"/mrtrix3"
  #     if not File.directory?("#{external_mrtrix_src_dir}")
  #       raise "not found: "+external_mrtrix_src_dir+". --with-copy_src_from_home is intended for developers only"
  #     end
  #     execute("rm -r *")
  #     execute("cp -r "+external_mrtrix_src_dir+" #{testpath}/mrtrix3")
  #   else
  #     execute("git clone https://github.com/MRtrix3/mrtrix3.git #{testpath}/mrtrix3")
  #   end

  #   cd "mrtrix3"
  #   githash = File.open("#{pkgshare}/git_hash") {|f| f.readline}
  #   execute("git checkout #{githash}")
  #   system "git", "log", "-1"
  #   # TODO: use config also for tests
  #   # cp "#{pkgshare}/config","config"
  #   # cp_r "#{prefix}/lib/", "lib"
  #   # mkdir "release"
  #   # cp "#{pkgshare}/config","release/config"
  #   begin
  #     execute("./configure -nogui")
  #     execute("./run_tests")
  #   rescue
  #     execute("echo 'Unable to run tests.")
  #   end
  #   execute("if tests failed: rerun with debug flag `brew test -d mrtrix3`, go to #{testpath} and inspect testing.log")
  #   system false # `brew test -d mrtrix3` will stop here
  #   # execute("cat testing.log")
  # end
end